parameter.txt

Author: Fei Lu
Email: flu@genetics.ac.cn; dr.lufei@gmail.com
Homepage: https://plantgeneticslab.weebly.com/

#This WGS SNP discovery pipeline are designed for both heterozygous and inbred species, especially the depth is high (e.g. >10X each taxon).
#To run and pipeline, the machine should have Java 8 and samtools installed. The lib directory should stay with FastCall.jar in the same folder. Command (e.g.): java -Xmx200g -jar FastCall.jar parameter.txt > log.txt &
#To specify reference, bam direcotory, chromosome, and output direcotory, please edit the the parameters below. Also, please keep the order of parameters.


#Parameter1:	Reference genome file with an index file (.fai). The reference should be in FastA format. Chromosomes are labled as 1-based numbers (1,2,3,4,5...).
/workdir/fl262/reference/cassavaV6_23Chr.fa

#Parameter2:	Bam directory, where your bam files are
/workdir/fl262/bam/

#Parameter3:	Taxa bam information file, including the info about what bams are included for each taxon
/workdir/fl262/taxaBamMap/taxaBamMap.txt

#Parameter4:	Chromosome on which genotyping will be performed (e.g. 1)
1

#Parameter5:	VCF output directory
/workdir/fl262/vcf